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- PDB-6ejn: The KLC2 TPR domain bound to the JIP3 leucine zipper domain -

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Basic information

Entry
Database: PDB / ID: 6ejn
TitleThe KLC2 TPR domain bound to the JIP3 leucine zipper domain
Components
  • C-Jun-amino-terminal kinase-interacting protein 3
  • Kinesin light chain 2
KeywordsTRANSPORT PROTEIN / kinesin JIP3 transport cargo molecular motor
Function / homology
Function and homology information


: / RHO GTPases activate KTN1 / Kinesins / anterograde axonal protein transport / COPI-dependent Golgi-to-ER retrograde traffic / positive regulation of neuron migration / respiratory gaseous exchange by respiratory system / MAP-kinase scaffold activity / lysosome localization / MHC class II antigen presentation ...: / RHO GTPases activate KTN1 / Kinesins / anterograde axonal protein transport / COPI-dependent Golgi-to-ER retrograde traffic / positive regulation of neuron migration / respiratory gaseous exchange by respiratory system / MAP-kinase scaffold activity / lysosome localization / MHC class II antigen presentation / JUN kinase binding / mitogen-activated protein kinase kinase kinase binding / axo-dendritic transport / axon regeneration / ciliary rootlet / mitogen-activated protein kinase kinase binding / kinesin complex / lung alveolus development / lung morphogenesis / axon development / microtubule-based movement / kinesin binding / regulation of JNK cascade / axolemma / smooth endoplasmic reticulum / vesicle-mediated transport / positive regulation of JUN kinase activity / JNK cascade / forebrain development / axon cytoplasm / positive regulation of neuron differentiation / post-embryonic development / axon guidance / protein localization / signaling receptor complex adaptor activity / cell body / growth cone / cytoplasmic vesicle / regulation of gene expression / microtubule / in utero embryonic development / neuron projection / lysosomal membrane / axon / Golgi membrane / dendrite / perinuclear region of cytoplasm / mitochondrion / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / Kinesin light chain / Kinesin light chain repeat / JNK/Rab-associated protein-1, N-terminal / RILP homology 1 domain / Kinesin light chain repeat. / RH1 domain / RH2 domain ...JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / Kinesin light chain / Kinesin light chain repeat / JNK/Rab-associated protein-1, N-terminal / RILP homology 1 domain / Kinesin light chain repeat. / RH1 domain / RH2 domain / RH1 domain profile. / RH2 domain profile. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Kinesin light chain 2 / Kinesin light chain / C-Jun-amino-terminal kinase-interacting protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsCockburn, J. / Hesketh, S.J. / Way, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal SocietyRG150205 United Kingdom
CitationJournal: Structure / Year: 2018
Title: Insights into Kinesin-1 Activation from the Crystal Structure of KLC2 Bound to JIP3.
Authors: Cockburn, J.J.B. / Hesketh, S.J. / Mulhair, P. / Thomsen, M. / O'Connell, M.J. / Way, M.
History
DepositionSep 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin light chain 2
B: Kinesin light chain 2
C: C-Jun-amino-terminal kinase-interacting protein 3
D: C-Jun-amino-terminal kinase-interacting protein 3


Theoretical massNumber of molelcules
Total (without water)82,7204
Polymers82,7204
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-50 kcal/mol
Surface area34710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.301, 163.301, 77.123
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Kinesin light chain 2 / Klc2 protein


Mass: 33051.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klc2, mCG_8395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91YS4, UniProt: O88448*PLUS
#2: Protein C-Jun-amino-terminal kinase-interacting protein 3 / JNK-interacting protein 3 / JNK MAP kinase scaffold protein 3 / JNK/SAPK-associated protein 1 / ...JNK-interacting protein 3 / JNK MAP kinase scaffold protein 3 / JNK/SAPK-associated protein 1 / JSAP1 / Mitogen-activated protein kinase 8-interacting protein 3 / Sunday driver 2


Mass: 8308.538 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk8ip3, Jip3, Jsap1, Syd2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ESN9

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 20% PEG 3350 0.2 M NaCSN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 3.2→77.123 Å / Num. all: 19393 / Num. obs: 19393 / % possible obs: 99.5 % / Redundancy: 7.9 % / Biso Wilson estimate: 88.97 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.113 / Rsym value: 0.105 / Net I/av σ(I): 6.4 / Net I/σ(I): 13.8 / Num. measured all: 152770
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.2-3.3781.5910.52242728210.5791.6981.5911.699.8
3.37-3.587.90.9120.92119026690.3310.9730.9122.999.8
3.58-3.827.90.4791.61993125090.1740.5110.4795.299.4
3.82-4.137.90.2453.11820123150.090.2620.2458.999.3
4.13-4.537.70.145.51661721590.0520.150.141499.6
4.53-5.0680.1116.91559519430.040.1190.11117.199.3
5.06-5.847.90.1126.81371117350.040.1190.11216.599.6
5.84-7.167.90.06810.91163914690.0250.0730.0682599.5
7.16-10.127.70.03119.1880911420.0120.0330.03148.999.1
10.12-77.1237.40.0242246506310.0090.0260.02459.397.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å67.71 Å
Translation3.2 Å67.71 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
SCALA3.3.22data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CEQ

3ceq


Resolution: 3.2→67.71 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.336
RfactorNum. reflection% reflectionSelection details
Rfree0.21 967 4.99 %RANDOM
Rwork0.191 ---
obs0.192 19373 99.1 %-
Displacement parametersBiso max: 252.42 Å2 / Biso mean: 127.28 Å2 / Biso min: 72.17 Å2
Baniso -1Baniso -2Baniso -3
1--3.469 Å20 Å20 Å2
2---3.469 Å20 Å2
3---6.938 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 3.2→67.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5207 0 0 0 5207
Num. residues----659
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1951SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes162HARMONIC2
X-RAY DIFFRACTIONt_gen_planes743HARMONIC5
X-RAY DIFFRACTIONt_it5279HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion670SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6077SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5279HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg7111HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion21.91
LS refinement shellResolution: 3.2→3.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3119 140 4.97 %
Rwork0.2636 2676 -
all0.266 2816 -
obs--99.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5041-1.70320.14257.9932-0.23361.39050.03670.04660.2250.03460.1070.1027-0.11490.4032-0.1437-0.2615-0.03710.1797-0.2311-0.0073-0.045451.4104-25.5432-0.4907
21.20212.02780.89825.5821.67020.2808-0.13910.0492-0.05290.20970.14740.04770.0549-0.014-0.0083-0.0414-0.05960.0336-0.3102-0.0593-0.163460.028450.23534.4459
31.1261-0.87860.07252.7602-0.5071.5948-0.1499-0.1153-0.16540.4964-0.13330.07250.10010.50410.2832-0.2463-0.0260.0392-0.19710.1823-0.029754.535411.70353.0277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|191 - A|477 }A191 - 477
2X-RAY DIFFRACTION2{ B|193 - B|477 }B193 - 477
3X-RAY DIFFRACTION3{ C|416 - C|475 }C416 - 475
4X-RAY DIFFRACTION3{ D|417 - D|477 }D417 - 477

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